This study evaluated the effects of applying a biofertilizer, alone and in combination with nanoparticles (NPs), under controlled greenhouse conditions to improve soil quality and wheat performance (soil from the region of General Cepeda, Coahuila, Mexico, was used). The integration of the biofertilizer with FexOx NPs proved particularly effective in enhancing soil physical and biological parameters as well as promoting superior crop growth compared with individual treatments. The incorporation of NPs markedly improved the biofertilizer's biocompatibility and stability, reinforcing its potential for optimizing plant nutrition, nutrient use efficiency, and overall agricultural sustainability. In addition, the combined treatments enhanced the utilization of native microbial diversity, thereby contributing to increased soil fertility and the quality and yield of crops in the study region. The best yield obtained in previous harvests (8.3 Mg ha-1) was improved to 8.48 Mg ha-1 with application of the biofertilizer with FexOx NPs. Moreover, shoot length increased significantly with the combination of the biofertilizer and ZnO NPs as well as with FexOx NPs separately, whereas root length was maximized with the addition of the biofertilizer alone. These findings underscore the synergistic effects of combining biofertilizers with metal-based nanoparticles to sustainably enhance wheat growth and productivity.